Quincy, a couple of quick questions.
1. Are you running the effects in series in the loop or in parallel?
2. Is this happening on all presets in the ModFactor? There is a way to set an output level per preset.
3. In general most people would put the ModF first, but obviously that's up to you, but sounds like the TF output is what you're looking for, and it's feeling the high MF output at the TF input. Just a general comment about effects ordering.
If you're running the EFX in series, then check to see if you have the global parameter set for yes on mix level. This could be jumping the volume/level up on every preset. If it's only happening on certain presets, then could be the output level.